Sun Oct 9 13:47:54 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph2.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb2.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Oct 9 2011 at 13:47:54 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2366 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.7072755 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): -1.431000 45.61700 ymin,ymax (A): 36.13200 86.46600 zmin,zma (A): -24.18600 25.24300 x,y,z range (A): 47.04800 50.33400 49.42900 scale (grids/A): 0.7072755 object centre (A): 22.09300 61.29900 0.5285006 number of atom coordinates read : 2366 total number of charged atoms : 2225 net assigned charge : 3.500020 assigned positive charge : 363.5892 centred at (gu) : 89.98058 89.98108 91.51826 assigned negative charge : -360.0895 centred at (gu) : 90.11207 90.09845 91.48122 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 8094 nv = 96 ne = 84 npr = 47632 no. pairs analyzed = 47632 no. exposed pairs = 2991 no. arc points = 20795 no. surface atoms = 998 nbur = 1368 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 507 mr = 4532 m= 3 mr = 72 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 4000 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1868 ## 168 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 8878 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.2848282E-09 6.7209520E-08 midg,1,midg; midg,igrid,midg 9.5254833E-08 -3.8180794E-08 1,midg,midg; igrid,midg,midg 1.0310951E-07 -4.6358100E-08 gauss-seidel spectral radius is 0.9896116 estimated iterations to convergence 80 setup time was (sec) 0.6800000 now iterating at: 13:47:55 rms-change max change #iterations 0.2198217 26.67235 at 10iterations 2.7283102E-02 3.670232 at 20iterations 4.0774853E-03 0.6307936 at 30iterations 9.5260836E-04 0.1614914 at 40iterations 3.1088275E-04 4.9552917E-02 at 50iterations finished qdiffx linear iterations at : 13:48:00 total time elapsed so far: 5.500000 # loops : 50 mean,max change (kT/e) : 3.1088275E-04 4.9552917E-02 energy calculations done at 5.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.670000 DelPhi exited at 13:48:01 5.676u 0.487s 0:06.42 95.7% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Oct 9 2011 at 13:48:01 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2366 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.121826 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): -1.431000 45.61700 ymin,ymax (A): 36.13200 86.46600 zmin,zma (A): -24.18600 25.24300 x,y,z range (A): 47.04800 50.33400 49.42900 scale (grids/A): 2.121826 object centre (A): 22.09300 61.29900 0.5285006 number of atom coordinates read : 2366 total number of charged atoms : 2225 net assigned charge : 3.500020 assigned positive charge : 363.5892 centred at (gu) : 89.94139 89.94301 94.55441 assigned negative charge : -360.0895 centred at (gu) : 90.33620 90.29512 94.44344 start vw surface at 0.1100000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 85662 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20795 grid for indexing accessible points = 1.400000 m= 33247 mr = 59826 m= 6099 mr = 24821 m= 523 mr = 3926 m= 11 mr = 261 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 315 time to turn everything in is 0.7600000 number of dielectric boundary points 36708 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 85 iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 17648 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.7072755 object centre at (A) : 22.09300 61.29900 0.5285006 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9496389E-02 2.4997264E-02 midg,1,midg; midg,igrid,midg 9.5623612E-02 -1.2830169E-02 1,midg,midg; igrid,midg,midg 7.7214977E-03 -1.2524275E-02 gauss-seidel spectral radius is 0.9988663 estimated iterations to convergence 235 setup time was (sec) 1.130000 now iterating at: 13:48:02 rms-change max change #iterations 5.049510 194.0317 at 10iterations 2.516917 84.35598 at 20iterations 1.261080 39.25104 at 30iterations 0.6333571 17.58240 at 40iterations 0.3167606 8.600224 at 50iterations 0.1590791 4.310213 at 60iterations 7.9900123E-02 2.270250 at 70iterations 4.0155265E-02 1.243622 at 80iterations 2.0300969E-02 0.6730728 at 90iterations 1.0384431E-02 0.2806168 at 100iterations 5.3892103E-03 0.1635132 at 110iterations 2.8907370E-03 9.1642857E-02 at 120iterations finished qdiffx linear iterations at : 13:48:15 total time elapsed so far: 13.52000 # loops : 120 mean,max change (kT/e) : 2.8907370E-03 9.1642857E-02 energy calculations done at 13.52000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.70000 DelPhi exited at 13:48:15 13.704u 0.523s 0:14.50 98.0% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Oct 9 2011 at 13:48:15 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2366 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.182739 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): -1.431000 45.61700 ymin,ymax (A): 36.13200 86.46600 zmin,zma (A): -24.18600 25.24300 x,y,z range (A): 47.04800 50.33400 49.42900 scale (grids/A): 3.182739 object centre (A): 22.09300 61.29900 0.5285006 number of atom coordinates read : 2366 total number of charged atoms : 2225 net assigned charge : 3.500020 assigned positive charge : 363.5892 centred at (gu) : 89.91197 89.91448 96.83139 assigned negative charge : -360.0895 centred at (gu) : 90.50431 90.44255 96.66516 start vw surface at 0.1200000 fill in re-entrant regions at 0.9100000 boundary points on vw surface= 197297 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20795 grid for indexing accessible points = 1.400000 m= 104817 mr = 144268 m= 41006 mr = 86265 m= 11262 mr = 33342 m= 2143 mr = 8519 m= 257 mr = 1508 m= 12 mr = 173 m= 0 mr = 3 time to grow re-entrant surface = 1.230000 no. cavity mid-points inaccessible to solvent = 1071 time to turn everything in is 2.300000 number of dielectric boundary points 82716 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.520000 number of grid points assigned charge 17798 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 2.121826 object centre at (A) : 22.09300 61.29900 0.5285006 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1076216 0.3682103 midg,1,midg; midg,igrid,midg 1.347288 -0.2396199 1,midg,midg; igrid,midg,midg 1.4151808E-02 -0.1077321 gauss-seidel spectral radius is 0.9993107 estimated iterations to convergence 300 setup time was (sec) 2.760000 now iterating at: 13:48:18 rms-change max change #iterations 11.34263 347.4775 at 10iterations 6.768299 146.5697 at 20iterations 4.038127 80.35555 at 30iterations 2.403378 42.61491 at 40iterations 1.424142 24.67277 at 50iterations 0.8428489 13.97653 at 60iterations 0.4989035 8.583023 at 70iterations 0.2944282 6.076955 at 80iterations 0.1737808 3.304750 at 90iterations 0.1025024 1.681667 at 100iterations 6.0526215E-02 1.036667 at 110iterations 3.5930246E-02 0.6385288 at 120iterations 2.1454684E-02 0.3793048 at 130iterations 1.3028090E-02 0.2317848 at 140iterations 8.1147738E-03 0.1606293 at 150iterations 5.2879890E-03 0.1006279 at 160iterations 3.6506080E-03 7.6286316E-02 at 170iterations 2.6901900E-03 5.5007935E-02 at 180iterations finished qdiffx linear iterations at : 13:48:40 total time elapsed so far: 24.23000 # loops : 180 mean,max change (kT/e) : 2.6901900E-03 5.5007935E-02 energy calculations done at 24.23000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 24.40000 DelPhi exited at 13:48:41 24.404u 0.561s 0:25.37 98.3% 0+0k 0+0io 0pf+0w